Variant report

Variant	rs6748816
Chromosome Location	chr2:54836340-54836341
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10180713	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1047499	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11885703	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11892788	0.81[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12104998	0.87[EUR][1000 genomes]
rs12105792	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12467581	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12468469	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12617036	0.85[EUR][1000 genomes]
rs12624153	1.00[CHB][hapmap]
rs12713260	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13016942	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1367295	0.87[EUR][1000 genomes]
rs1510611	0.87[JPT][hapmap]
rs1541854	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs168506	0.82[EUR][1000 genomes]
rs171350	0.84[EUR][1000 genomes]
rs17344072	0.89[EUR][1000 genomes]
rs17521078	0.83[EUR][1000 genomes]
rs1864493	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2048371	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2271322	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2292356	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2292357	0.92[EUR][1000 genomes]
rs2931463	0.87[EUR][1000 genomes]
rs2931464	0.87[EUR][1000 genomes]
rs2941583	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2941586	0.93[CEU][hapmap];0.81[CHB][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2941587	0.93[CEU][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2941591	0.88[EUR][1000 genomes]
rs2941595	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2971875	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2971877	0.93[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2971879	0.93[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2971883	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2971887	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3106204	0.88[EUR][1000 genomes]
rs354213	0.86[EUR][1000 genomes]
rs354226	0.83[EUR][1000 genomes]
rs354228	0.85[EUR][1000 genomes]
rs354231	0.92[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs3796014	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4233952	0.81[EUR][1000 genomes]
rs4444573	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4455199	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4519562	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4592889	0.87[EUR][1000 genomes]
rs4671221	0.83[EUR][1000 genomes]
rs4671222	0.84[EUR][1000 genomes]
rs4671225	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4671226	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4671945	0.83[EUR][1000 genomes]
rs4671946	0.85[EUR][1000 genomes]
rs4671947	0.85[EUR][1000 genomes]
rs4671949	0.87[EUR][1000 genomes]
rs4671951	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4671955	0.84[EUR][1000 genomes]
rs4671956	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4671960	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4671961	0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4990319	0.85[EUR][1000 genomes]
rs6545411	0.81[EUR][1000 genomes]
rs6545413	0.81[EUR][1000 genomes]
rs6545414	0.81[EUR][1000 genomes]
rs6545415	0.81[EUR][1000 genomes]
rs6545418	0.82[EUR][1000 genomes]
rs6545419	0.83[EUR][1000 genomes]
rs6545427	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6545429	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6545434	0.93[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6704769	0.84[EUR][1000 genomes]
rs6706372	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6724590	0.82[EUR][1000 genomes]
rs6729826	0.86[EUR][1000 genomes]
rs6731661	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6732949	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6734658	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6735813	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742607	0.80[EUR][1000 genomes]
rs6746306	0.82[EUR][1000 genomes]
rs6760298	0.87[JPT][hapmap]
rs6761369	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6761398	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7558950	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7563706	0.82[EUR][1000 genomes]
rs7589236	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7598568	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7607451	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs907135	0.87[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6748816	EML6	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54824800-54839200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr2:54827200-54839000	Weak transcription	Hela-S3	cervix
3	chr2:54827600-54839200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:54827600-54839200	Weak transcription	Dnd41	blood
5	chr2:54829800-54859800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:54830800-54839200	Weak transcription	Esophagus	oesophagus
7	chr2:54831000-54837800	Weak transcription	Osteobl	bone
8	chr2:54831200-54838000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:54831400-54837000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:54832200-54838200	Enhancers	Brain Hippocampus Middle	brain
11	chr2:54832200-54839200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:54832200-54839200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:54832200-54839200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:54832200-54840800	Weak transcription	K562	blood
15	chr2:54832400-54837200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:54832400-54839200	Weak transcription	Placenta	Placenta
17	chr2:54832400-54843400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:54832400-54843800	Weak transcription	Brain Germinal Matrix	brain
19	chr2:54832600-54837200	Weak transcription	HSMMtube	muscle
20	chr2:54832600-54839200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:54832800-54839000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr2:54832800-54839600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:54833000-54836600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:54833000-54837800	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:54833000-54839400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:54833000-54839400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:54833000-54839400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:54833000-54839600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:54833000-54841000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:54833200-54836600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:54833200-54836600	Weak transcription	Small Intestine	intestine
32	chr2:54833400-54838800	Weak transcription	Primary B cells from cord blood	blood
33	chr2:54833400-54843400	Weak transcription	Fetal Brain Male	brain
34	chr2:54833600-54836600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:54833600-54839200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:54833600-54839200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:54833600-54839200	Weak transcription	Psoas Muscle	Psoas
38	chr2:54833600-54839600	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:54833600-54840000	Weak transcription	Fetal Kidney	kidney
40	chr2:54833800-54836400	Weak transcription	Aorta	Aorta
41	chr2:54833800-54836600	Weak transcription	Gastric	stomach
42	chr2:54833800-54836600	Weak transcription	Stomach Mucosa	stomach
43	chr2:54833800-54837600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr2:54833800-54837800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:54833800-54838800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:54833800-54839200	Weak transcription	Thymus	Thymus
47	chr2:54833800-54839200	Weak transcription	NHEK	skin
48	chr2:54833800-54839200	Weak transcription	NHLF	lung
49	chr2:54833800-54840800	Weak transcription	HMEC	breast
50	chr2:54834000-54836600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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